gl.report.reproducibility {dartR.base}

Reports summary of RepAvg (repeatability averaged over both alleles for each locus) or reproducibility (repeatability of the scores for fragment presence/absence)

Description

SNP datasets generated by DArT have an index, RepAvg, generated by reproducing the data independently for 30 of alleles that give a repeatable result, averaged over both alleles for each locus. In the case of fragment presence/absence data (SilicoDArT), repeatability is the percentage of scores that are repeated in the technical replicate dataset.

Usage

gl.report.reproducibility(
  x,
  plot.display = TRUE,
  plot.theme = theme_dartR(),
  plot.colors = NULL,
  plot.dir = NULL,
  plot.file = NULL,
  verbose = NULL
)

Arguments

x

Name of the genlight object containing the SNP or presence/absence (SilicoDArT) data [required].

plot.display

Specify if plot is to be produced [default TRUE].

plot.theme

Theme for the plot. See Details for options [default theme_dartR()].

plot.colors

Vector with two color names for the borders and fill [default c("#2171B5", "#6BAED6")].

plot.dir

Directory to save the plot RDS files [default as specified by the global working directory or tempdir()]

plot.file

Filename (minus extension) for the RDS plot file [Required for plot save]

verbose

Verbosity: 0, silent or fatal errors; 1, begin and end; 2, progress log; 3, progress and results summary; 5, full report [default 2, unless specified using gl.set.verbosity].

Details

The function displays a table of minimum, maximum, mean and quantiles for repeatbility against possible thresholds that might subsequently be specified in gl.filter.reproducibility. If plot.display=TRUE, display also includes a boxplot and a histogram to guide in the selection of a threshold for filtering on repeatability. If plot.file is specified, plots are saved to the directory specified by the user, or the global default working directory set by gl.set.wd() or to the tempdir(). For examples of themes, see:

• https://ggplot2.tidyverse.org/reference/ggtheme.html and

• https://yutannihilation.github.io/allYourFigureAreBelongToUs/ggthemes/

Value

An unaltered genlight object

Author(s)

Custodian: Arthur Georges – Post to https://groups.google.com/d/forum/dartr

See Also

gl.filter.reproducibility

Other matched report: gl.report.callrate(), gl.report.hamming(), gl.report.locmetric(), gl.report.maf(), gl.report.overshoot(), gl.report.pa(), gl.report.rdepth(), gl.report.secondaries(), gl.report.taglength()

Examples

 
# SNP data
  out <- gl.report.reproducibility(testset.gl)
  
# Tag P/A data
  out <- gl.report.reproducibility(testset.gs)